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Subject:

Re: FLIRT problem..

From:

Steve Smith <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Sun, 23 Apr 2006 08:27:13 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (353 lines)

That's right - for reasons that no-one seems to understand, the TCL  
GUIs can't output text to the terminal under the Cygwin  
version......hohum.

Cheers, Steve.



On 22 Apr 2006, at 21:56, Martin M. Monti wrote:

> Mark,
>
> I tried it with the old version of FSL installed on the cluster  
> here, and it worked (i.e. gave me the output code). It could just  
> be that the installation of the new version, which instead is on my  
> personal computer (via Cygwin), has some parameter off..
>
> cheers, thanks for all the help!
>
> Martin
> ----- Original Message ----- From: "Martin M. Monti"  
> <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Saturday, April 22, 2006 4:26 PM
> Subject: Re: [FSL] FLIRT problem..
>
>
>> Mark,
>>
>> yes I thought that should have been the case, but in fact I don't  
>> get the command line output in my shell..
>>
>> ideas?
>>
>> martin
>> ----- Original Message ----- From: "Mark Jenkinson"  
>> <[log in to unmask]>
>> To: <[log in to unmask]>
>> Sent: Saturday, April 22, 2006 12:15 PM
>> Subject: Re: [FSL] FLIRT problem..
>>
>>
>>> Dear Martin,
>>>
>>> You can specify arbitrary precision for the voxel size in mm, but  
>>> the
>>> number of voxels has to be an integer.  So given that this rarely  
>>> works
>>> out exactly, I would round up normally to make sure that you don't
>>> truncate anything.
>>>
>>> As for the commands - if you look in the terminal where you
>>> start the ApplyXFM gui from, then it will display the complete
>>> set of commands that were run.
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>> On 22 Apr 2006, at 16:16, Martin M. Monti wrote:
>>>
>>>> Mark,
>>>>
>>>> Very clear, thanks - it worked out great!
>>>>
>>>> Two (minor) lingering questions: is it a problem if i specify a  
>>>> FOV with decimals? (having a high res FOV of 256*256*176, I'd  
>>>> need a  FOV of 85.34*85.34*44 to be specified in applyXFM).
>>>>
>>>> Also, is there anywhere I can see what is the code that comes  
>>>> out  of this (I'm trying to script away as much of this as  
>>>> possible..!)  - something like the report.log or anywhere that  
>>>> can help me  tranform this into a code?
>>>>
>>>> Thanks for the help!
>>>>
>>>> Martin
>>>> ----- Original Message ----- From: "Mark Jenkinson"  
>>>> <[log in to unmask]>
>>>> To: <[log in to unmask]>
>>>> Sent: Saturday, April 22, 2006 4:50 AM
>>>> Subject: Re: [FSL] FLIRT problem..
>>>>
>>>>
>>>>> Dear Martin,
>>>>>
>>>>> Which image did you take the values from?
>>>>> What you want is the low resolution of the EPI and the FOV of the
>>>>> *anatomical* image.  Note that FOV (Field of View) is not the
>>>>> number of voxels, it is the size of the whole image in mm.    
>>>>> Therefore,
>>>>> you want to figure out what this is for the anatomical image (by
>>>>> multiplying the voxel size by the number of voxels - separately in
>>>>> each dimension) and then figure out how many voxels this would
>>>>> be at your new resolution (by dividing by the voxel size).
>>>>>
>>>>> For example, if the EPI is 3*3*4mm per voxel with 64*64*33 voxels
>>>>> but the anatomical is 2*2*2mm per voxel with 100*110*80 voxels
>>>>> then they have FOVs of 192*192*132mm and 200*220*160mm
>>>>> respectively.  This means that to get the anatomical FOV at the
>>>>> EPI resolution you need to have voxels that are 3*3*4mm big
>>>>> but have (200/3)*(220/3)*(160/4) = 67*74*40 voxels in total.
>>>>> These are the numbers that you'd need to feed into ApplyXFM.
>>>>>
>>>>> Hope this is now clear.
>>>>> All the best,
>>>>> Mark
>>>>>
>>>>>
>>>>> On 21 Apr 2006, at 17:07, Martin M. Monti wrote:
>>>>>
>>>>>> Hi Mark,
>>>>>>
>>>>>> still nothing..! I tried using the applyXFM GUI, and set  
>>>>>> voxel  size 3x3x3.9900000095 and FOV 64x64x33, both taken  
>>>>>> straight off  avwhd.
>>>>>> Yet when I then apply the transf matrix to my lowres I still  
>>>>>> get  it off to the side, as before..
>>>>>>
>>>>>> I 'm a bit puzzled at this point..
>>>>>>
>>>>>> Do you have other suggestions? Or, is there a way I can  
>>>>>> upload  the images and get you to try it?
>>>>>>
>>>>>> cheers
>>>>>>
>>>>>> Martin
>>>>>> ----- Original Message ----- From: "Mark Jenkinson"  
>>>>>> <[log in to unmask]>
>>>>>> To: <[log in to unmask]>
>>>>>> Sent: Friday, April 21, 2006 10:21 AM
>>>>>> Subject: Re: [FSL] FLIRT problem..
>>>>>>
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> Glad that this has helped.
>>>>>>>
>>>>>>> One thing to note still is that if the FOV of BH_sample_EPI  
>>>>>>> is smaller
>>>>>>> than the FOV of BH_anat_bet then you will end up with off  
>>>>>>> centre or
>>>>>>> truncated images like you had before.  If this is the case  
>>>>>>> and  you still
>>>>>>> want the low res then I suggest using the ApplyXFM gui and   
>>>>>>> selecting
>>>>>>> the voxel size and number of voxels (and hence FOV) manually.
>>>>>>>
>>>>>>> All the best,
>>>>>>> Mark
>>>>>>>
>>>>>>>
>>>>>>> On 21 Apr 2006, at 15:15, Martin M Monti  
>>>>>>> ([log in to unmask]) wrote:
>>>>>>>
>>>>>>>> Mark, Steve,
>>>>>>>>
>>>>>>>>  thanks, it hadn't occurred to me that the default is  
>>>>>>>> 12dof!  (doh!)
>>>>>>>>
>>>>>>>> Re Mark's point though, I actually want the registered  
>>>>>>>> image  (the output) to have the same low resolution as my  
>>>>>>>> sample_EPI  (which  is the same as the initial resolution of  
>>>>>>>> BH_EPI), can I  then  just use sample_EPI as the reference  
>>>>>>>> in the second step  (i.e.  when I apply the matrix created  
>>>>>>>> by registering  sample_EPI to the  anatomical)?
>>>>>>>> So like this:
>>>>>>>>
>>>>>>>> flirt -in BH_sample_EPI -ref BH_anat_bet -omat BH_mat2anat - 
>>>>>>>> dof 7
>>>>>>>> flirt -in BH_EPI -ref BH_sample_EPI -applyxfm -init  
>>>>>>>> H_mat2anat  -out
>>>>>>>> BH_EPI_reg2
>>>>>>>>
>>>>>>>>  Thanks for the help!
>>>>>>>>
>>>>>>>>  Martin
>>>>>>>>
>>>>>>>> ----- Original Message -----
>>>>>>>> From: Mark Jenkinson <[log in to unmask]>
>>>>>>>> Date: Friday, April 21, 2006 3:10 am
>>>>>>>> Subject: Re: [FSL] FLIRT problem..
>>>>>>>> To: [log in to unmask]
>>>>>>>>
>>>>>>>>> Dear Martin,
>>>>>>>>>
>>>>>>>>> Using the first flirt command will only generate a single  
>>>>>>>>> output
>>>>>>>>> volumeas that is our normal usage.  I thought that it would  
>>>>>>>>> do  the
>>>>>>>>> same as
>>>>>>>>> the -applyxfm option and generate a 4D output, but it  
>>>>>>>>> doesn't.  I
>>>>>>>>> guessthat we don't use it in this mode so we've never noticed.
>>>>>>>>>
>>>>>>>>> Using the -applyxfm option will generate a 4D output  
>>>>>>>>> though,  so the
>>>>>>>>> second form is what you want, but you need a different  
>>>>>>>>> reference
>>>>>>>>> volumeif you want it to have the same output size as an
>>>>>>>>> anatomical.  So the
>>>>>>>>> commands you want are:
>>>>>>>>>
>>>>>>>>> flirt -in BH_sample_EPI -ref BH_anat_bet -omat BH_mat2anat - 
>>>>>>>>> dof 7
>>>>>>>>> flirt -in BH_EPI -ref BH_anat_bet -applyxfm -init  
>>>>>>>>> BH_mat2anat - out
>>>>>>>>>
>>>>>>>>> BH_EPI_reg2
>>>>>>>>>
>>>>>>>>> Note that in the first line you use the -dof 7 option, as  
>>>>>>>>> in your
>>>>>>>>> first form,
>>>>>>>>> and in the second line you use the image BH_anat_bet as your
>>>>>>>>> reference,since this controls the output voxel resolution  
>>>>>>>>> and  FOV.
>>>>>>>>>
>>>>>>>>> This works fine for me, but if you have a lot of timepoints in
>>>>>>>>> BH_EPI
>>>>>>>>> then the
>>>>>>>>> output image will be *huge* and this might be why it is  
>>>>>>>>> hanging
>>>>>>>>> for you.
>>>>>>>>> In this case you should check how big you expect the  
>>>>>>>>> output  to  be and
>>>>>>>>> see if that is causing problems with the available RAM/swap.
>>>>>>>>>
>>>>>>>>> All the best,
>>>>>>>>> Mark
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 21 Apr 2006, at 01:26, Martin M. Monti wrote:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>>  I'm trying to simply register an EPI to an anatomical. Very
>>>>>>>>> easy
>>>>>>>>>> you'd say, yet..
>>>>>>>>>>
>>>>>>>>>> I used the sample code on the website, but I get either of 2
>>>>>>>>> problems:> Either only one volume is in the output image  
>>>>>>>>> (if I do
>>>>>>>>> the
>>>>>>>>>> registration directly, as in the First Method), or the image
>>>>>>>>> looks
>>>>>>>>>> awefully off (if I use method two - also straight from the  
>>>>>>>>>> website).
>>>>>>>>>>
>>>>>>>>>> First method:
>>>>>>>>>> 1) flirt -in BH_EPI -ref BH_anat_bet -out BH_EPI_reg -omat
>>>>>>>>>> BH_mat2anat -dof 7 -v
>>>>>>>>>> This gives me as output a SINGLE volume, resampled at the
>>>>>>>>>> resolution of the anatomical, although (according to slices)
>>>>>>>>> well
>>>>>>>>>> aligned.
>>>>>>>>>>
>>>>>>>>>> Second method:
>>>>>>>>>> 1) flirt -in BH_sample_EPI -ref BH_anat_bet -omat BH_mat2anat
>>>>>>>>> [Get
>>>>>>>>>> the matrix by transforming a ONE volume EPI image (the
>>>>>>>>> sample_EPI)
>>>>>>>>>> to the Anatomical]
>>>>>>>>>> 2) flirt -v -in BH_EPI -ref BH_sample_EPI -applyxfm -init
>>>>>>>>>> BH_mat_F1toAnat -out BH_EPI_reg2 [Apply the matrix]
>>>>>>>>>>
>>>>>>>>>> This one gives the correct voxel size, correct number of
>>>>>>>>>> timepoints, but when I open it with FSLView it's off to  
>>>>>>>>>> the side
>>>>>>>>>
>>>>>>>>>> (seehttp://webmartin.altervista.org/flirt.htm for a picture
>>>>>>>>>> comparison of before and after using FLIRT - although no  
>>>>>>>>>> obvious
>>>>>>>>>
>>>>>>>>>> diffwrence when I look into avwhd for the pre and post FLIRT
>>>>>>>>>> images), with the right (left) side being cut off  
>>>>>>>>>> slightly, and
>>>>>>>>> the
>>>>>>>>>> top slice being in fact still several slices away (in the Z
>>>>>>>>>> direction) from the top of the brain. Unfortunately I  
>>>>>>>>>> can't open
>>>>>>>>> it
>>>>>>>>>> with slices and overlay it to the anatomical given that  
>>>>>>>>>> they are
>>>>>>>>> of
>>>>>>>>>> different sizes.
>>>>>>>>>>
>>>>>>>>>> I tried using the high_res image as the -ref, in step (2)  
>>>>>>>>>> of the
>>>>>>>>>
>>>>>>>>>> second method but it hangs on me..
>>>>>>>>>>
>>>>>>>>>>  Can I get a little help please?
>>>>>>>>>>
>>>>>>>>>>   Cheers
>>>>>>>>>>
>>>>>>>>>>  Martin
>>>>>>>>>>
>>>>>>>>>> PS: should you think it's relevant this is how I obtained the
>>>>>>>>>> BH_EPI image:
>>>>>>>>>>
>>>>>>>>>> avwroi subjectEPI_bet subjectEPI_del 4 83
>>>>>>>>>> slicetimer -i subjectEPI_del -o subjectEPI_slct -r 2 --
>>>>>>>>> ocustom=../
>>>>>>>>>> Slice_Order.txt -v
>>>>>>>>>> mcflirt -in subjectEPI_slct -out BH_EPI -dof 6 -verbose 1 -
>>>>>>>>> stages 4
>>>>>>>>>> -report
>>>>>>>>>>
>>>>>>>>>> --------------------------
>>>>>>>>>> "Upward, not Northward!" [Edwin Abbott - FlatLand]
>>>>>>>>>>
>>>>>>>>>> I became insane, with long intervals of horrible sanity.   
>>>>>>>>>> [E.A. Poe]
>>>>>>>>>>
>>>>>>>>>> Would you tell me, please, which way I ought to go from here?
>>>>>>>>>> ''That depends a good deal on where you want to get to.''  
>>>>>>>>>> Said
>>>>>>>>> the
>>>>>>>>>> Cat. I don't much care where -- Said Alice. Then it doesn't
>>>>>>>>> matter
>>>>>>>>>> which way you go, said the Cat. [Lewis Carroll]
>>>>>>>>>>
>>>>>>>>>> Che si trattasse di una gara? ..Un colpo il mondo e un  
>>>>>>>>>> colpo tu,
>>>>>>>>> a
>>>>>>>>>> chi stupiva un po' di piu'.. [Per Un Vecchio Bambino -  
>>>>>>>>>> Roberto
>>>>>>>>>> Vecchioni]
>>>>>>>>>>
>>>>>>>>>> --------------------------------------------
>>>>>>>>>> Martin M. Monti
>>>>>>>>>> Princeton University
>>>>>>>>>> Department of Psychology
>>>>>>>>>> Green Hall 3-S-8
>>>>>>>>>> (609) 258-5679
>>>>>>>>>> www.webmartin.net
>>>>>>>>>> --------------------------------------------
>>>>>>>>>>
>>>>>>>>>
>>>


------------------------------------------------------------------------ 
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------ 
---

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